MI6, aka SIS (Secret Intelligence Service), was a branch of the British government concerned with foreign intelligence. Like its domestic counterpart MI5, it was sometimes simply called the Secret Service. Kim Philby explained to the Eighth Doctor that despite the fact the two organisations were theoretically working on the same side in two separate spheres, MI6 and MI5 frequently clashed. (PROSE: Endgame) On another occasion, the Doctor told Leighton Woodrow he had believed that MI6 had no jurisdiction within Britain's borders, a belief that Woodrow found refreshingly naive. (COMIC: The Fallen)

In 1963, an MI6 agent called Barker secretly worked with Russian spies, in particular a man who went by the alias of Miles Barrington Smythe. On 23 November, Miles left secret documents for Barker which instructed him to use his government employee card to access information in William Pike's cab before being arrested by the Police. Barker questioned Bill Pike, who was also arrested, although he was interrupted by K9 Mark 2, Jorjie Turner and Starkey. K9 was able to prove Bill's innocence by scanning the document and finding the instructions involving the use of a government employee card, Bill was let free as he wasn't a government agent. K9 almost exposed Barker although the document self-destructed before he could find his name. Barker and Miles later met up where Barker gave him a spare copy of the document. (TV: The Cambridge Spy)